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A six-plex proteome quantification strategy reveals the dynamics of protein turnover.

ABSTRACT: MS1 full scan based quantification is one of the most popular approaches for large-scale proteome quantification. Typically only three different samples can be differentially labeled and quantified in a single experiment. Here we present a two stages stable isotope labeling strategy which allows six different protein samples (six-plex) to be reliably labeled and simultaneously quantified at MS1 level. Briefly in the first stage, isotope lysine-d0 (K0) and lysine-d4 (K4) are in vivo incorporated into different protein samples during cell culture. Then in the second stage, three of K0 and K4 labeled protein samples are digested by lysine C and in vitro labeled with light (2CH3), medium (2CD2H), and heavy (2(13)CD3) dimethyl groups, respectively. We demonstrated that this six-plex isotope labeling strategy could successfully investigate the dynamics of protein turnover in a high throughput manner.

SUBMITTER: Wang F

PROVIDER: S-EPMC3650664 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

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A six-plex proteome quantification strategy reveals the dynamics of protein turnover.

Wang Fangjun F Cheng Kai K Wei Xiaoluan X Qin Hongqiang H Chen Rui R Liu Jing J Zou Hanfa H

Scientific reports 20130101

MS1 full scan based quantification is one of the most popular approaches for large-scale proteome quantification. Typically only three different samples can be differentially labeled and quantified in a single experiment. Here we present a two stages stable isotope labeling strategy which allows six different protein samples (six-plex) to be reliably labeled and simultaneously quantified at MS1 level. Briefly in the first stage, isotope lysine-d0 (K0) and lysine-d4 (K4) are in vivo incorporated ...[more]

PMID: 23661174

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A six-plex proteome quantification strategy reveals the dynamics of protein turnover.

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A six-plex proteome quantification strategy reveals the dynamics of protein turnover.

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